## [1] "Max fold diff lib size = 1.75956241223834"
## [1] "57820 total transcripts. Keeping 17782 transcripts after filtering"
Heirarchical clustering based on expression profile Spearman correlations. This shows that the data are overall high quality (no outliers), with good grouping of samples within-cell lines. The biggest difference is clearly between colon and ovarian cell lines.
Comparing distribution of log-counts per million per sample looks reasonable
## `summarise()` has grouped output by 'samp_pert', 'cell_line'. You can override
## using the `.groups` argument.
## # A tibble: 6 × 4
## # Groups: samp_pert, cell_line [6]
## samp_pert cell_line perturbation BIRC6_GE
## <chr> <chr> <chr> <dbl>
## 1 HCC15.sgBIRC6.1 HCC15 sgBIRC6.1 5.68
## 2 HCC15.sgBIRC6.4 HCC15 sgBIRC6.4 5.61
## 3 HCC15.sgCh2.2 HCC15 sgCh2.2 6.66
## 4 HCC202.sgBIRC6.1 HCC202 sgBIRC6.1 6.16
## 5 HCC202.sgBIRC6.4 HCC202 sgBIRC6.4 5.78
## 6 HCC202.sgCh2.2 HCC202 sgCh2.2 7.00
Collapse replicates
Save LCPM data (rep collapsed)
Collapse across replicates by summing read counts Model cell line as random effect
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## [1] "Running gene-permutation testing with 1000000 perms"
## [1] "Running gene-permutation testing with 1000000 perms"
## [1] "Running gene-permutation testing with 1000000 perms"
## [1] "Running gene-permutation testing with 1000000 perms"
## [1] "Running gene-permutation testing with 1000000 perms"
## [1] "Running gene-permutation testing with 1000000 perms"
Estimated KO effect in Dependent - Independent lines
## [1] "Running gene-permutation testing with 1000000 perms"
## [1] "Running gene-permutation testing with 1000000 perms"
## [1] "Running gene-permutation testing with 1000000 perms"
## [1] "Running gene-permutation testing with 1000000 perms"
## [1] "Running gene-permutation testing with 1000000 perms"
## [1] "Running gene-permutation testing with 1000000 perms"
#model individual cell line effects
## [1] "Running gene-permutation testing with 1000000 perms"
## [1] "Running gene-permutation testing with 1000000 perms"
## [1] "Running gene-permutation testing with 1000000 perms"
## [1] "Running gene-permutation testing with 1000000 perms"
## [1] "Running gene-permutation testing with 1000000 perms"
## [1] "Running gene-permutation testing with 1000000 perms"
## [1] "Running gene-permutation testing with 1000000 perms"
## [1] "Running gene-permutation testing with 1000000 perms"
## [1] "Running gene-permutation testing with 1000000 perms"
## [1] "Running gene-permutation testing with 1000000 perms"
## [1] "Running gene-permutation testing with 1000000 perms"
## [1] "Running gene-permutation testing with 1000000 perms"
## [1] "Running gene-permutation testing with 1000000 perms"
## [1] "Running gene-permutation testing with 1000000 perms"
## [1] "Running gene-permutation testing with 1000000 perms"
## [1] "Running gene-permutation testing with 1000000 perms"
## [1] "Running gene-permutation testing with 1000000 perms"
## [1] "Running gene-permutation testing with 1000000 perms"
## Rows: 50 Columns: 8
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## Delimiter: ","
## chr (2): pathway, leadingEdge
## dbl (6): pval, padj, ES, NES, nMoreExtreme, size
##
## ℹ Use `spec()` to retrieve the full column specification for this data.
## ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
## Rows: 50 Columns: 8
## ── Column specification ────────────────────────────────────────────────────────
## Delimiter: ","
## chr (2): pathway, leadingEdge
## dbl (6): pval, padj, ES, NES, nMoreExtreme, size
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## ℹ Use `spec()` to retrieve the full column specification for this data.
## ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
## Rows: 50 Columns: 8
## ── Column specification ────────────────────────────────────────────────────────
## Delimiter: ","
## chr (2): pathway, leadingEdge
## dbl (6): pval, padj, ES, NES, nMoreExtreme, size
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## ℹ Use `spec()` to retrieve the full column specification for this data.
## ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
## Rows: 50 Columns: 8
## ── Column specification ────────────────────────────────────────────────────────
## Delimiter: ","
## chr (2): pathway, leadingEdge
## dbl (6): pval, padj, ES, NES, nMoreExtreme, size
##
## ℹ Use `spec()` to retrieve the full column specification for this data.
## ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
## Rows: 50 Columns: 8
## ── Column specification ────────────────────────────────────────────────────────
## Delimiter: ","
## chr (2): pathway, leadingEdge
## dbl (6): pval, padj, ES, NES, nMoreExtreme, size
##
## ℹ Use `spec()` to retrieve the full column specification for this data.
## ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
## Rows: 50 Columns: 8
## ── Column specification ────────────────────────────────────────────────────────
## Delimiter: ","
## chr (2): pathway, leadingEdge
## dbl (6): pval, padj, ES, NES, nMoreExtreme, size
##
## ℹ Use `spec()` to retrieve the full column specification for this data.
## ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
## Rows: 50 Columns: 8
## ── Column specification ────────────────────────────────────────────────────────
## Delimiter: ","
## chr (2): pathway, leadingEdge
## dbl (6): pval, padj, ES, NES, nMoreExtreme, size
##
## ℹ Use `spec()` to retrieve the full column specification for this data.
## ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
## Rows: 50 Columns: 8
## ── Column specification ────────────────────────────────────────────────────────
## Delimiter: ","
## chr (2): pathway, leadingEdge
## dbl (6): pval, padj, ES, NES, nMoreExtreme, size
##
## ℹ Use `spec()` to retrieve the full column specification for this data.
## ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.